|
| Status |
Public on Feb 23, 2022 |
| Title |
Lung_CUT_TAG_PRMK_rep1_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
genotype/plasmids: U6-sgTrp53-FES-mCherry-P2A-puro/U6-sgRb1-FES-mCherry-P2A-puro/U6-sgKmt2c-FES-mCherry-P2A-puro/MSCV-Myc-IRES-Luc2/U6-sgMeis2-FES-mCherry-P2A-puro
replicates: Lung_PRMK_rep1_H3K4me3
antibody: H3k4me3 1:50 (#ab8580, Abcam)
|
| Treatment protocol |
RNA-Seq: Treated with SAM and Vehicle in PRMK organoids
WGBS: PRM and PRMK tumor tissue were harvested from the recipient mice. The PRM and PRMK tumor tissue were harvested from the recipient mice at ~3-4 mouths after transplantation.
|
| Growth protocol |
CUT-TAG: The PRM and PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.
RNA-Seq: The PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.
WGBS: The PRM and PRMK mouse were developed on recipient mice after transplantation through injection into the left lobe of lung.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT-TAG: PRMK lung organoids were harvested from the recipient mice.
RNA-Seq: RNA was extracted with Trizol
CUT&TAG assay was performed using NovoNGS® CUT&TAG 2.0 High-Sensitivity Kit (Novoprotein scientific Inc., Cat# N259-YH01-01A).
WGBS: After in situ transplantation, lung organoids carrying Trp53 and Rb1 mutations and Myc overexpression lead to single primary PRM in recipient mice. And lung organoids carrying Trp53 ，Rb1 and kmt2c mutations and Myc overexpression lead to single primary PRMK in recipient mice.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
library strategy: CUT&TAG
|
| Data processing |
CUT-TAG:
Sequenced reads were mapped to mm10 whole genome using bowtie2
peaks were called using SEACR
RNA-Seq:
Sequenced reads were mapped to mm10 whole genome using STAR_2.6.0a
Counts were normalized by DESeq2
WGBS:
WGBS reads were aligned to the mm10 genome assembly using BS-Seeker2(v2.1.8)
Bismark was used to call methylation
Genome_build: mm10 or GRCm38
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: txt files with gene normalised by DESeq2
Supplementary_files_format_and_content: CGmap.gz files for WGBS
|
| |
|
| Submission date |
Dec 02, 2021 |
| Last update date |
Apr 01, 2022 |
| Contact name |
Xaingyu Pan |
| E-mail(s) |
pangxueyu233@outlook.com
|
| Organization name |
Sichuan University
|
| Department |
State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.
|
| Lab |
Chen & Liu Lab
|
| Street address |
No.17 Renming road section3
|
| City |
Chengdu, Cihna |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE161570 |
KMT2C Loss Promotes Small Cell Lung Cancer Metastasis through DNMT3A-mediated Epigenetic Reprogramming |
|
| Relations |
| BioSample |
SAMN23572350 |
| SRA |
SRX13287725 |
